Shinji, Weapon X
by Aneirin
Summary: X-Men/Evangelion crossover. Shinji's father created the only weapons able to stand up to the Angels, and only a mutant can pilot them... based mostly on the manga. Shinji x Rei, eventual OOC.
1. hunted

Disclaimer: I own neither Evangelion or the X-Men. I did come up with this story however. So, it's mine.

Author's note: What's happenin' ya'll? Yes, I have a new story. I'll get back to Shinji Saga soon enough, worry not. However, I've had this idea in my head for more than a year. Imagine my surprise when days after I have this idea, Gunman posts a story with a similar idea. I haven't read his for fear of copying something, but I might get to it eventually.

Anywho, this is mostly based on the manga, as I needed an angrier Shinji to work with. I refuse to be any less vague on this point! To those who can't figure it out, too bad! Mwuahahaha! But seriously, here we go!

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The boy ran through the forest, his eyes darting from side to side. No sign of an ambush. He stopped at a tree, climbing swiftly up before catching his breath. He ran a hand through his brown hair, thinking of the events of the last hour. His neighbors had found out his secret, and had started to chase him as soon as home was out of sight. They couldn't do anything with his aunt and uncle around. God forbid they risk the life of normal people while trying to catch a-

The boy froze. He heard the mob now, loading rifles. He could smell the gunpowder too. No time to stop. He had to keep going. He jumped to the next tree, swinging off of a branch to the next tree. They'd have a hard time catching him with no tracks to follow.

888

All was calm. The railway guns stood motionless on the tracks. The only sounds were made by the gulls. The men knew that beneath the water lurked a terrifying monster, the worst they'd ever imagined. And the worst any of them would ever see. They couldn't exactly see the dark shape in the water, but they knew it was coming...

BABOOM! Something erupted from the water!

888

"Unidentified object in Ocean Sector!" a voice exclaimed. "Routing images to main monitors! Confirmed On Visual!"

"It's been fifteen years, hasn't it?" a voice asked a sitting figure. The sitting figure's glasses shone in the darkness.

"Yes," he said. "There's no mistake. It's an Angel!" He was silent for a moment. Then he said, "The day has finally arrived... The time of Trials that humanity cannot avoid..."

888

The boy walked into the city, having evaded the mob. Stupid ignorant people. Couldn't stand anything different. Afraid of everything they couldn't understand! It made him so angry sometimes. He could've fought back. He could've taken every one of them. But if he did, he'd prove them right, at least in their eyes. He found a pay phone and walked over to it, thinking he should probably call his Aunt and Uncle to let them know he was okay.

"**This is the emergency broadcast system**," said a voice, most likely from a speaker system. "**Stand by for important alert!** **A special state of emergency is being declared at 12:30 PM for entire center Kanto District, with the Tokai District at the epicenter. All residents should quickly and calmly evacuate to their designated shelters. We repeat, at 12:30 today...**"

The boy put down the phone. "Huh," he said, "The phones are out. The monorails aren't running either. How'm I supposed to make my appointment now?" He sighed, walking to a nearby flight of stone steps and sitting down. 'I wonder what all that stuff about 'shelters' is. Don't tell me a war's been declared or something like that...'

He pulled an envelope and a picture out of his chest pocket. The note in the envelope had mentioned his father. 'Father...' he thought, grimacing. 'He abandoned me more than ten years ago. Just dumped me on my Aunt and Uncle. What on Earth can he want from me now?' He pulled out the picture Sweatdrop He blushed slightly looking at it. The picture was of a purple-haired woman, probably in her late twenties, wearing the skimpiest outfit he'd seen on a woman. She was bending over towards the camera, the index and fingers on her left hand forming 'v'. On it was a note: 'To Shinji

I'm going to pick you up, so please wait for me!' There was an arrow pointing to her... chest, with the words 'P.S. Note the cleavage!' with a little hear drawn next to it. It looked like she had kissed the picture right under the note.

'What a weird lady,' he thought. 'And she's my father's what?' He put the picture and the envelope back in his pocket. "Nothing to do," he said, "But walk the last two stations." Suddenly, Shinji heard jets. He looked up, seeing four flying overhead. "What the," he said, "Aren't those flying a bit low?" Suddenly, one launched a missile! It flew just yards above Shinji's head."

"Cruise missiles!?" he exclaimed. He followed to where the missile was headed. It was a giant monster! "What the hell is **that**!?" The missiles had no effect on the thing. Suddenly, it raised an arm. A blast erupted from the middle of a three "fingered" hand, ripping through one of the planes. Shinji ran, just avoiding the crashing vehicle.

Skreeee! A car screeched to a halt right next to him. The door flew open. It was the woman from the picture! Misato Katsuragi!

"Sorry to keep you waiting Shinji!" she said. "C'mon! Get in!"

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Yeah... not much room for creativity n this chapter. But, it's the first, and as you know by now if you've read my stuff, the first chapter is always short. The next one will be much longer and much more original. Promise!


	2. angels and demons

Disclaimer: I own neither Evangelion or the X-Men. I did come up with this story however. So, it's mine.

Author's note: Wowee! Took long enough. Going on, let's see, one, two... several months. I'm sorry. Things happened, I just didn't work on it, excuses excuses. Thing is, I finally got the first volume of the show. It totally renewed my interest in Evangelion, and it got me thinking about both Apprentice and this story here. So, I finished my half finished Apprentice chapter(which had been that way since the end of school) and decided I should work on the next chapter of this as well. I've been avoiding it due to having to copy some things from the manga directly, something I'm not thrilled about. But, I've worked this around some and now can make it more original. In fact, I'll be able to reduce relying on the manga a great deal pretty soon, or so I hope.

So, without further ado, on with the show!

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"Hurry!" exclaimed Misato, the monster getting closer to their position.

"Okay!" exclaimed Shinji, jumping into the car. Misato floored it, taking off before Shinji even had the door all the way shut. It closed, and Shinji quickly put on his seatbelt.

"Sorry I'm late," said Misato, eyes glued to the road.

"N-no," said Shinji, the sound of explosions filling the air behind them, "I'm the one who was late." Another explosion sounded.

"The entire tank force was wiped out," said Misato. Shinji couldn't quite read her expression, her shades being too dark to see her eyes. "The army's throwing everything they've got at that thing. The missiles aren't even affecting it!"

"What is it, anyway?" asked Shinji.

"You seem pretty calm, all things considering," said Misato.

"Yeah?" asked Shinji. Misato nodded.

"That thing," she explained, "Is an 'Angel'."

"Angel?" asked Shinji, confused. "No kind of Angel I've ever heard of." Suddenly, one of the missiles fired at the Angel veered off course, ricocheting off of a building.

"Oh no!" exclaimed Misato, quickly trying to turn the car away and head in a new direction. The missile hit right behind them, exploding and flipping the car over. Misato groaned. "Are you okay?"

"Yeah," said Shinji, upside down. Suddenly, the car was covered in shadow. A giant hand reached down and grabbed the car. "Another one!?"

"No!" exclaimed Misato, "This one's on our side!" The hand put the car back right-side up. Shinji looked out the window to see what it was, but he couldn't get a good look at it. All he could tell was that it was human-like in shape, and that it was the biggest moving thing he'd ever seen. There were suddenly several crashes in succession, sounding like giant footsteps.

"The Angel's coming!" exclaimed Misato. The giant thing turned to the Angel. It balled it's hands into fists. Suddenly, three long blades extended from each hand. Shinji's eyes widened.

"Whoa," he said. "That's just like-"CRASH! The Angel tackled the giant, sending it crashing into a nearby building.

"Hang on!" said Misato, flooring it once more. As she dodged the debris in the street, Shinji kept watching the battle behind them. Actually, it was all around them. The two fighters were so large that almost everything they did covered a massive amount of distance. No matter how far away Misato got them, the battle seemed to get there in no time. The giant was taking a severe beating.

"Our guy's getting clobbered," said Shinji, worried.

"Not for long," said Misato, her eyes still invisible. Cloud's began forming overhead. They quickly became dark storm clouds. Suddenly, a huge bolt of lightning struck the Angel, momentarily paralyzing it. The clouds moved downwards, becoming a fog around the giant, who kneeled down. The mist cleared, and the Giant was gone.

"What was that?" asked Shinji. "What's up with that weather?"

"No Time to explain," said Misato, "We need to keep going."

888

"Pilot's heart rate and blood pressure dropping!" exclaimed a techy. "Neural interface down 5!"

"She's hemorrhaging through the chest plate seems!" cried another.

"Three minutes until N2 detonation!" announced a third.

"Call it back," said the man with the shining dark glasses. "It can't be helped." The mist gave the Giant on screen cover as a hatch opened. The Giant was taken underground on a large metal platform. The hatch closed just as the mist cleared.

888

Shinji looked back at the city. "All the planes are clearing out," he said. "Did they give up?"

"Oh no!" exclaimed Misato, seeing something in her review mirror. "Tuck your head in your lap and brace for impact!"

Suddenly there was an explosion larger than Shinji could have ever imagined. The car, though miles from the city, began to leave the road. Misato grabbed on to Shinji to try and protect him. The car flipped straight over.

888

"Ha!" exclaimed a military man. "We got it!" They watched the explosion on screen, the military man, his two comrades, and the man in dark glasses and his team. "Did you see that!? That's the power of our N2 mines!" The man in glasses simply watched the now static filled screen grimly, the light reflecting off of his glasses and hiding his expression. "Do you know what this means? The Eva's are unnecessary!"

"Still standing by for target destruct confirmation," said a techy.

"An explosion of that force?" asked an older military man. "Can there be any doubt?" Suddenly, there was a loud beeping from one of the monitors.

"The energy readings just spiked!" exclaimed a techy.

"WHAT!?"

"Visuals back online!" The screen showed a gigantic crater with a small black object in the center. The screen zoomed in, and the military men paled. The Angel slowly stood up. The mine had done nothing to it, except reveal a second face growing from the chest.

"Our trump card for nothing," said the first military man. "We sacrificed all of Tokyo-2. That thing is a monster... a demon..."

"Yes,"said a third military man, talking on a telephone. "Understood." Click. He looked at the man. "HQ has just transferred authority for this operation to you, Ikari. Let's see what you're capable of."

"We'll be frank," said the older gentleman. "The U.N. army admits that our weapons were ineffective against the target. But, do you really think you can do much better?"

"Do not be concerned," said Commander Ikari, standing up with an unnoticeable limp. He turned to face the three men. He pushed his glasses up the bridge of his nose, just moving them out of the glare and revealing his eyes. "After all, this is the purpose of NERV.

888

"Ugh," grunted Shinji, ignoring the broken glass around him. He turned his head, coming face-to-face with Misato's chest. He blushed. "A-are you alright M-Miss Katsuragi?"

"I... I can't take this anymore..." whimpered Misato, her shades having fallen from her eyes. She looked somewhere between dazed and on the verge of tears. They crawled out of the car. Misato helped Shinji up. "You okay?" she asked.

"Yeah," said Shinji, putting his hand to his forehead.

"AAAHH!" screamed Misato, causing Shinji to jump. "No! The body's riddled with shrapnel! And I had 33 payments left on her!" She looked down. "Damn it! My favorite dress, ruined! I'll never get these stains out!" She bent down, picking up what used to be her sun glasses. "And my shades are ruined to boot." She hung her head in defeat.

'What a strange lady,' thought Shinji. She turned to face him.

"Oh my God!" she exclaimed, rushing to grab him. "Shinji are you okay?"

"Huh?" asked Shinji, blinking.

"You're bleeding!" Sure enough, there was a good amount of blood on Shinji's forehead, and on his hand.

"Whoa!" exclaimed Shinji. He wiped his hand across his forehead again. He wiped off all of the blood. Misato waited for him to keep bleeding, but nothing happened. "Did I get it off?"

"Uh, yeah," said Misato, slowly. "Are you in pain? Do you feel any more bleeding?" Shinji shook his head, wiping the blood off of his hands.

"It might have just looked bad," said Shinji. "It could have been one of those small cuts that heal up really fast."

"I guess," said Misato. "Come on. Help me with this." She and Shinji grabbed the car, and began to tip it over. "We still have a schedule to keep."

888

The car was on a special platform, which moved down a large hallway. Misato sat in the driver's seat, reapplying her lipstick.

"NERV?" asked Shinji, looking at the manual he'd been given.

"Yep," said Misato, putting the final touches on her make-up. "A special agency under the direct control of the U.N. I work there as an international civil servant, same as your father." Shinji smirked.

"So you're in the 'admirable job of defending humanity' too?" asked Shinji.

"What's with the sarcasm?"

"What's so great about humanity?" asked Shinji. Misato looked a bit confused. "Never mind." They rode on in silence for a bit, until Shinji finally asked the question that had been burning in his mind from the beginning. "Miss Katsuragi?"

"Misato's fine," she answered. "But what's up?"

"Why did my father call me here?" asked Shinji. "I thought he'd forgotten about me."

"You should ask him that yourself," said Misato. Shinji looked down at his lap. "You're not comfortable around your father, are you?" Shinji shook his head. They suddenly reached the end of the hallway. The rail was now taking them through a gigantic, dome covered area. Shinji looked out the window in awe. Above them were buildings, and below was a lush green forest with a pyramid in the center.

"Whoa!" exclaimed Shinji. "Is this a real geofront?"

"Mhmm," answered Misato. "NERV H.Q. The stronghold of humanity, and the key to resurrecting the world!"

888

"Haaah! Haaah! Haaah!" The blue haired girl's labored breathing pained even the medical team that was rushing her down the hallway on the Gurney. She had bandages over one eye, and a cast on her arm.

"Pilot has suffered severe injuries!" exclaimed one doctor. "There's a possibility of splenic rupture!"

"The LCL is causing interference!" explained a second. "She can't-"

"We can see that!" shouted a third. "Just hurry and get her to the medical bay now! We need to get as much LCL out as possible before we can help her!" He put an oxygen mask on her face to help her breath. It would take everything they had to help her pull through.

888

"The U.N. is beating a full retreat," said the older man who had been with Ikari earlier. "What do you plan to do?"

"We'll simply have to reinitialize Unit 1," said Ikari.

"But Gendo!" exclaimed the older man. "Rei can't go again! We have no pilot!"

"No need for concern," said Gendo, watching a screen. It showed a purple haired woman leading a brown haired boy down a hallway. "One has just been delivered."

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Boom! And we're getting ready for it! I wanted the battle to be in this chapter, but I felt that it would be better to wait or this chapter would be too long, and too much would have been going on. Besides, I wanted to get it done and get it to you guys. Of Course, I might go and combine this with the first chapter. Tell me what you think.

So yeah, next time I'll reveal some more. What is the LCL disrupting? Was Shinji's wound really small enough to just heal up that fast? And where'd the lightning come from? Answers next time. Stay tuned.


	3. conflict

Disclaimer: Evangelion and X-Men are not mine. However, this is the story I have come up with. So there's that.

Author's Note: Holy... just... wow. Anyone waiting for this to get updated, thank you for your patience. You can all thank a good friend of mine for this update, and the numerous others that will be uploaded at about the same time. She gave me a deadline and a condition for failure, and that got me working. So, here I go. I sure hope my writing improved since last I used it.

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After somewhere near what Shinji estimated as half an hour, he finally spoke up. "We're lost aren't we?" he asked.

"N-no," stammered Misato. "I... I definitely know where we're going."

'You're a bad liar,' Shinji thought to himself. They came to an elevator door with a map next to it, and Misato studied it carefully.

"Hmm," she said, thoughtfully, "if we keep going down this hallway, we should be able to-" She was cut off by a sudden dinging noise from the elevator. The door opened and a blonde woman in a lab coat stepped out.

"For Heaven's sake," said the blonde woman, coming extremely close to Misato, "Will you two just follow me? You're very late." Misato stepped back with a small embarrassed smile.

"Sorry Rits," she said. The woman merely shook her head and turned to Shinji.

"You're the young Ikari, correct?" she asked, flashing a smile. Was it Shinji's imagination, or did this woman's canine teeth seem unusually long and sharp?

"Y-yes," he said, trying not to let on that he was staring.

"Come with me," she ordered, and they both stepped into the elevator with her.

888

Gendo watched the scene unfold on one of the security screens. "Fuyutsuki," he said to the older man, "You take it from here. I have something important to take care of." Gendo took a few steps forward and held out his hand. A bar shot up from a hidden slot in the floor. He grabbed it and the whole section of floor, a small platform, began descending. As the hole left behind was covered with a hidden door, Fuyutsuki looked to the men and women at their terminals.

"Call first wave to battle stations," said the older gentleman, "and prep the Eva."

888

"ALL FIRST WAVE PERSONNEL TO BATTLE STATIONS!" exclaimed the voice over the intercom. "ALL FIRST WAVE PERSONNEL TO BATTLE STATIONS!"

Shinji, Misato, and the woman in the lab coat, who had introduced herself as Ritsuko Akagi, were all in a small motorboat on an underwater lake.

"Battle Stations!" exclaimed Misato. "Are they crazy! They can't be ready this soon. What are they supposed to do about a pilot? Rei can't-"

"It's been taken care of," Ritsuko cut in. Misato looked at her incredulously, then looked back at Shinji. Shinji missed Misato shaking her head as he turned to look at Ritsuko.

"Pilot for what?" asked Shinji.

"You'll see in just a moment," said Ritsuko. The boat docked at a small staircase. They got out and climbed up to a door. They stepped through into a dark room. Shinji suddenly saw a glimmer of something, but not in the room. At least, he didn't think it could be in the room.

He saw a girl with alabaster skin, red eyes, and blue hair, standing directly before him, but only for a moment. He blinked and she was gone. He shook his head and blinked a few more times. 'What was that?' he thought.

"Are you paying attention?" asked Ritsuko, turning back to Shinji.

"Uh, yes ma'am," said Shinji, now focusing on the blonde doctor in front of him.

"Good," said Ritsuko, "cause you don't want to miss a minute of this." She looked forward again, into the blackness. "Lights!"

The lights came on, temporarily blinding Shinji. When his vision cleared, he gasped. "The robot!" he exclaimed. The giant purple armored face from before was staring at him, the rest of the machine submerged in liquid.

"Close," said Ritsuko. "This is indeed what you saw earlier, but it's no robot. This, Shinji, is the last line of defense for humanity. Artificial Human Evangelion, or Eva Unit 1!" Shinji was dumbstruck once more at the size of the thing in front of him. He'd felt dwarfed before when it picked up the car. But now, seeing it this close...

"Is... is this my father's work?" asked Shinji.

"Yes," came a voice Shinji hadn't heard in years. All three looked up to see Gendo Ikari, standing in a room above them overlooking the area. "It's been a while."

"Father," said Shinji. The boy narrowed his eyes slighty.

"Shinji," said Gendo, "please listen to me very carefully. This is what is going to happen. You are going to get into the Eva. You are going to battle the Angel." Shinji was speechless.

"What!" Misato exclaimed. "You can't be serious! It took Rei seven months to sync with Unit 1! He just got here! There's no way we can-"

"Enough!" Gendo said. "I'm only expecting him to get inside it at this point. Nothing more. Now Shinji, if you please."

"..." Shinji said nothing.

"Shinji?"

"...No."

"What?"

"NO!" yelled Shinji. His eyes burned with anger as he looked up at his father. "You think you can just leave me out there for all those years, surrounded by people that hate me, and then just ask me to come and save you when it's convenient! You really think you can just ask me to risk my life like it's no big deal!"

'What is he talking about?' thought Misato. 'Does he mean what I think?'

"Yes," said Gendo. "It's for the good of humanity. Now, if you please, I will have you escorted into the Eva." Two armed guards stepped into the room, and began walking towards Shinji. Misato stepped between them and Shinji.

"Now hang on just a minute!" she exclaimed.

"Ma'am," said one of the guards, quickly and carefully grabbing her and pushing her out of the way. She went to retaliate, but was stopped by Ritsuko, who grabbed her arm. Misato looked at her angrily, but Ritsuko just calmly shook her head.

"Son," said one of the guards, now inches from Shinji. He put his hand out to grab his shoulder. "If you'll please-"

SHRRRRRRKT! The room froze as three long, sharp bones erupted from each of Shinji's hands. The sound of tearing flesh echoed in the room for a moment. The two guards were frozen in place.

'He is,' thought Misato. 'He's a mutant!'

"I said NO!" roared Shinji, turning on the men. He put his arms out, taking a very aggressive stance. He slashed at them. "Get AWAY!" the two men jumped back, just barely avoiding the razor tipped bones. Shinji was breathing heavily, and his anger was all too apparent in his eyes. He turned back towards his father. "You can't make me! You can't make me do anything!"

There was silence in the room, broken only by Shinji's heavy, enraged breaths. No one spoke, no one moved. Everything was at a standstill. Finally, the elder Ikari spoke.

"Oh but I could," said Gendo. "However, in this case I won't. Nothing would come of it. Fine, don't get in the Eva. Feel free to go home, then. You are of no use to me. Coward." He activated the intercom. "Bring in Rei."

"Can you use her?" asked Fuyutsuki over the connection.

"She isn't dead," answered Gendo.

Slllkt. The bones receded into Shinji's hands, the flesh between his knuckles healing almost right away. Shinji straightened out a bit, hanging his head as he got his breathing under control. Ritsuko shook her head, and then went into action.

"Recalibrate the systems on Unit One for Rei again," she called to the technicians waiting nearby. "Let's move, people!" Misato walked over to Shinji, and put a hand on his shoulder to calm him.

"I..." he muttered, "I'm sorry, miss Misato, I just..." she applied some pressure to his shoulder, as if to say she understood. She was about to say something when they became aware of the sound of squeaking wheels. They both looked to the right, and saw a gurney being wheeled in. Shinji's eyes went wide.

On the gurney was the girl he'd seen in his head. An IV was attached to her arm, and even from this distance he could hear her labored breathing. She had a cast on one arm, and an eyepatch over one eye. She didn't look like she was in a state to do anything.

"Rei," said Gendo, "our only backup is useless. You will have to pilot the Eva."

"Yes... sir...," the girl managed to say. She slowly, painfully began to sit up. Shinji could barely watch, her pain evident to all present. He could even hear the strain she was putting on herself, or at least he thought he could.

Suddenly there was a series of loud, metallic clanging noises. "That noise!" exclaimed Misato, as everyone present looked towards the ceiling.

"The Angel," said Gendo. "It's found us."

888

Above and away, just outside the city, the Angel's eyes glowed with power. There was a sudden intensity, and then beams shot forth into the Tokyo 3. KATHOOOM!

888

There was a great rumbling, and pieces of the ceiling began to fall down, the force of the explosion above ground rocking the geofront. Something large crashed into the rook of the complex they were housed in, and it shook light fixtures and pieces of the ceiling free. Debris came crashing down towards the floor. To Shinji's horror, two light fixtures came crashing down around the girl, and knocked her off of the gurney.

He moved faster than he remembered ever moving before, and was able to catch her before she fell hard to the ground, shielding her from falling rubble.

"Hey," he said, holding her so that her face was towards his, "hang in there!" If she could hear him, she didn't respond, only able to pant, the pain of falling while so injured having likely robbed her of the ability to speak.

'This is wrong,' thought Shinji. 'It's one thing for him to ask me to pilot that thing... but her? She can't.'

"Shinji," said Misato, cutting into his thoughts. "Do you see now? We need you. You have to pilot the Eva, or that girl... that poor girl will have to. You knew there was a reason you were called here. You knew it wasn't just to reconnect with your dad. Just... if you don't... she will. Don't you have any shame? Any sense of honor?"

"Stop wasting your breath," said Gendo. "There's no point in wasting any more time on him, Captain. Shinji! If you aren't going to help, then leave!"

"..." Shinji clenched his eyes shut. "Rrrrgh... fine." He kept his voice calm, not wanting to disturb the girl he now held in his arms, who appeared to have lost conciousness. "I'll pilot it. Better me than her." He carefully laid the girl down.

"Shinji," Misato said quietly as the young man stood up.

"Well said, Shinji," said Misato, walking over to him. "Now please, follow me." He did as he was told, taking one look back at his father as he went. Gendo smiled.

888

Shinji was now sitting inside what they'd called the Entry Plug. It felt strange. The whole chamber smelled. It was a familiar smell, but one he couldn't place. He had been assured that it was clean, that it was decontaminated after each session, but his sensitive nose was still picking something up. He ignored it for the time being.

'I'm not afraid to die,' he thought. 'And I will not let my father call me a coward. He may have just said it to get a rise out of me, but I'll show him.' He grimaced. 'He hasn't needed me ever. But now he's built some kind of robot that needs me? This is ridiculous.'

Notifications began blaring over the intercom, both inside the cockpit and out in the facility. "COOLING CYCLE COMPLETE! ALL INTERNAL CAGE SYSTEMS IN DOCKING POSITION! PILOT HAS REACHED COCKPIT POSITION WITHIN ENTRY PLUG!" Shinji felt the entire cockpit move.

"ROGER! INSERTING ENTRY PLUG!" Shinji felt the cockpit lowering, but just barely felt it. He was also aware the instant it locked into place. Now the only intercom he was aware of was inside the cockpit.

"Plug lock-in procedure complete!" exclaimed a female voice. "Initiating Level One Interface! Flooding Entry Plug!"

'Flooding?' thought Shinji. 'Did she say-?' Suddenly there was a noise like rushing water. An orange-gold liquid began filling the cockpit!

"What!" exclaimed Shinji. He held his breath. 'Are they trying to drown me!' He almost unsheathed his claws, considering trying to tear his way out, but he knew it would likely be futile.

"Shinji!" came Ritsuko's voice over the intercom. "Calm down! That liquid is called LCL. Once it saturates your lungs, you'll have direct oxygen transfer. You'll be fine!"

"Says you!" Shinji retorted before filling his lungs with air again.

"Just chill out!" exclaimed Misato's voice this time. "You'll get used to it! Just relax!" Shinji held his breath as long as he could, but it all came bursting out of him. He found that, against all instincts, he could breath in the LCL, but it felt wrong. He identified the smell now. It was faint, but it reminded him of blood.

'At this rate I'll have died of a heart attack before I even get out there to fight the Angel,' thought Shinji, his mind beginning to calm.

"Main power connected!" came the female voice over communications. "All circuits functioning properly! Initiating power up sequence! Opening reciprocal circuits!" At that moment the cockpit changed, where Shinji had been staring at a blank wall, suddenly, there were lights and shapes. Then, all at once, he could see in front of him. Or rather, he deduced, whatever the Eva was seeing.

"First contact all clear!" the voice continued. "A10 Nueral Synapses operating within normal limits!"

"Incredible!" exclaimed Ritsuko. "This is going to work!"

"Synchro error ratio within 0.3%," said Misato. "Unit One! Prepare to Launch!"

* * *

WOOOOOOO! First chapter in several years folks! Sorry about the wait. I just... things happened. But don't worry, the friend I mentioned (who you can all thank in the comments if you'd like) has made a deal with me that will keep me working. This may not get updated right away, but I will be updating stories in general weekly. And don't worry about quality, because these stories have been brewing in my head for quite a while now (years). I got this.

Special note: this will be updated almost immediately after. Sorry I didn't have the battle in here like I said it would years ago, but that made the chapter feel too long. It'll be in the next chapter, I promise.

Stay tuned!


	4. fury

Disclaimer: Evangelion and X-Men are not mine. However, this is the story I have come up with. So there's that.

Author's Note: BAM! The first of my promised weekly updates. This story may not get updated weekly, but it is likely to get updated quite often. So without further ado, here is that battle I've been promising ya'll!

* * *

Unit 1 lurched as it suddenly stopped upon reaching the surface. A panel in what Shinji understood to be a false building opened up, and Shinji was treated to a view of the city, and of something else. The Angel was right in front of him.

For a moment, panic seized him. He was face to face with the enemy, and he had no idea how to control the machine he'd been sent out to fight it in.

"Shinji!" came Misato's voice. "Shinji listen!"

"Huh?" asked Shinji.

"Listen," said Ritsuko. "I know we didn't get time to train you on how to operate the Eva, so consider this a crash course. Begin by walking forward."

"How?" exclaimed Shinji.

"Just imagine walking!" answered the scientist. "Imagine walking, and the Eva will walk. Trust me!"

"A-alright," said Shinji. He tried thinking about walking. It didn't work at first. Suddenly the Eva took a step forward, catching him off guard. It halted for a moment, and then continued as he refocused his thoughts. The Angel didn't react, but Shinji didn't want to get too close before he knew what he was doing.

"Okay," he said, mostly to himself. "Stop." The Eva continued walking. "Stop." Still, Unit 1 continued to walk. "Stop!" Nothing changed. Shinji's temper flared a bit. "To hell with it!" He thought about charging forward, and the Eva complied almost immediately.

"Shinji wait!" exclaimed Misato. But it was too late. Eva Unit 1 charged forward at the Angel, who raised it's own arm in response. Not knowing what to expect, Shinji raised his arms, and to his surprise the Eva mimicked his actions. However, to what he wasn't sure was his relief or embarrassment, the Eva completely ran past the Angel

"I missed!" he exclaimed.

"Shinji watch out!" cried Misato.

"Huh?" *CRASH* The Eva crashed straight into a building, and then fell to the ground. "Ugh." Shinji tried to pull himself, and by extension the Eva, up from the ground.

"GWUAAAAAAAAAR!" came a roar from behind him. It was the Angel.

"Shinji get up!" exclaimed Misato. "You can do this!" Quick as a flash, the Angel's taloned arm shot out and grabbed Unit 1 by the head, and hauled it up. It grabbed Unit 1's arm and began applying pressure. Shinji felt it! It was as if the Angel had grabbed his arm!

"Shinji you have to get out of there!" ordered Misato.

"I-I can't!" answered Shinji, the pain in his arm growing. Suddenly there was a snapping and crushing noise. The Angel had just crushed the Eva's forearm, and pulled on it, hard.

"AUGH!" yelled Shinji.

"Shinji calm down!" came Misato's voice. "That wasn't your arm that the Angel dislocated, it was the Eva's!"

"THEN WHY AM I FEELING IT?" exclaimed Shinji.

888

"This can't be happening," muttered Ritsuko back at the headquarters. Realizing she'd spoken allowed, she kept her mouth shut. 'The sync ratio can't be this high, unless... did it go into hyper fluctuation?' She looked to one of the people on computers, a young woman named Maya. "Can you lower the neural feedback regulators a notch? No, wait try for two!"

"I'll try!" answered Maya. She punched the appropriate keys, and then blanched. "IT'S NOT WORKING!"

888

It smashed the Eva against the building again, and began generating a strange hum. It was an energy buildup.

"SHINJI GET OUT OF THE WAY!" screamed Misato.

*ZSHOOM!* Shinji felt a horrendous piercing pain in his eye.

"AAAAAAAUGH!" he roared in agony. The Angel repeated the attack several times, an energy javelin continuously piercing the Eva's head. The Angel took Unit 1 and pointed it at another building, charged once more and fired, shooting the Evangelion into a building several hundred yards away.

888

The technicians of NERV were in a panic. "CRANIAL AREA GOING INTO PARALYSIS!" shouted one.

"Cutting power to control neurons!" exclaimed another, typing rapidly.

"OVERFLOW!" warned another. "It isn't working!"

"Oh God, what about Shinji?" exclaimed Misato.

"I don't know," answered Ritsuko. "Right now we can't tell if he's alive or dead. The Eva has fallen silent."

"Eject the plug then!" cried Misato. "We have to get him out of there!"

"We can't!" Ritsuko shot back. "We've lost all contact! There's nothing we can do!"

888

Shinji was still breathing, of that he was sure. He was also in pain. More pain than he'd ever been in. It was like he'd been stabbed in the eye. However, his thoughts began to muddy. The pain was too much. It was driving him over the edge. He growled as his vision went red.

"RAAAAAAAAAAAAAAAGH!" roared the Eva, suddenly standing back up. The Angel, who had assumed it's foe dead, turned back around to face him. It was impossible to gage what the Angel was thinking, if it could think, by either of the two masks imbedded in it's chest.

*SNAP* Unit 1's arm suddenly sprang back to it's former shape, even snapping the crushed armor plating back to it's correct form.

"Shinji?" asked Misato over the intercom. "What's happening?" She recieved no answer. There was a sudden noise of metal unsheathing, cutting through the city air.

"Progressive Claws have been activated!" exclaimed Ritsuko's voice. "We didn't teach him that! What is happening? Shinji? SHINJI?" She too recieved no answer.

"WAAAAAAAAAAAARRGH!" roared Unit 1, charging at the Angel. The beast did not have time to react as Unit 1 slashed off one of it's arms. It drove the second set of claws into the Angel.

The Angel shook violently under the force of the blow, and grabbed Unit 1, trying to pry it off. Unit 1 slashed it across both masks, and then began tearing at what appeared to be the creature's rib cage. It tried prying the monster's torso open, but the Angel fought back.

888

"Dear God!" exclaimed Ritsuko. "I get it now! The Eva is out of control! The Unit has gone berserk!"

"Can't we do anything?" asked Misato.

"Negative," answered Maya. "All connection has been severed with the Unit. It has rejected all override commands."

"Storm," said Gendo. "Intervene. Shock the creature, it seemed to stun it last time."

"But sir!" she answered. "Shinji's right there! If I try that I could fry Unit 1 too!"

"She is right," said Fuyutsuki. "Risking Unit 1 now would be foolish. Let it get clear, and then she can strike."

"...Fine," answered Gendo. "But the second you can, take the shot. Begin preparing now."

"Yes, sir."

888

Clouds began forming over the city, concentrating on the battle sight. Neither combatant noticed, however. Unit 1 had just successfully pried open it's opponent's chest, when suddenly a field shot out.

It looked like a force-field, glowing a yellow orange. It blasted Unit 1 back, causing it to crash to the ground. The Angel slowly picked itself up, and began advancing on the Eva.

Unit 1 got up, let out a loud growl, and charged forward with a roar. It dove into the energy field claws first, and began stabbing. To the surprise of the NERV workers watching the battle from inside their headquarters, the blades began to pierce the shield.

"The Angel has an AT Field too," said Ritsuko's voice over the Eva's communicator. As before, she received no answer.

Unit 1 tore a hole in the so-called AT Field, and pounced on the Angel. It had spotted it's target: the large red orb protruding from the Angel's now heavily damaged chest. With a deft movement, the enraged Unit knocked away the Angel's defending arms and thrust its claws into the red sphere.

There was a great crashing noise as the thing cracked. Chunks of it fell away. The Angel's eyes suddenly glowed. It grappled Unit 1, wrapping it's arms and legs around the Eva. The hum returned, louder than ever.

"IT'S GOING TO SELF-DESTRUCT!" shouted Misato. "SHINJI, MOVE!"

There was a flash of light and an explosion. Energy shot all around, inexplicably forming a cross at the dead center of the whole thing. the people watching on screen were nearly blinded by the light. Then, the light began to dim, and there was fire all around, smoke obscuring their vision.

Then movement was detected. A large humanoid figure was walking through the flames. It was Eva Unit 1. It stopped as the smoke began to clear away.

"Life signs confirmed for both pilot and Eva!" exclaimed a technician's voice over the communicator.

"Deploy retrieval team immediately!" ordered Misato's voice.

Shinji sat there in the Eva's cockpit, completely still, and utterly unaware of anything happening around him.

888

Shinji awoke with a start in a hospital bed. He'd had a very strange dream. It wasn't about the Eva, he was sure that had been real. What had it been? He tried to catch snatches of it as it drifted away from him. His mother. Surely he'd seen his mother. Hadn't he?

He shook his head and tried to stand up. He made it to his feet, only to suddenly feel lightheaded. He wobbled a bit, unsteady. He placed his hand on the bed-rail and took a few deep breaths. His ears picked up a faint sound coming down the hallway. A faint sound that was accompanied by a slightly familiar scent.

He walked to the door and entered the hallway. He looked over to see a gurney being wheeled towards him. It was the girl with the blue hair, Rei. She had multiple doctors surrounding her, checking her vitals and keeping her IV steady.

Her eye met his for a brief moment as she passed. He looked after her, and saw his father standing a ways down the hall. He stopped the gurney and bent over to check on the girl. He looked Shinji's way for a moment, and their eyes met. It lasted only a moment, and then Gendo turned away, and he and the gurney proceeded down the hall.

"Such a cold man," said a voice behind him. Shinji had been so lost in thought that he hadn't heard or smelled Misato coming. "Surely his battle-weary warrior, his own son, deserves a kind word or two."

"He's never been one to praise me," said Shinji, turning to greet her. "Why are you here Misato?"

"I came to pick you up, of course," she answered, smiling. "I heard you were feeling better. You don't know how worried I was about you."

"Thanks," said Shinji, turning to walk down the hall, not wanting her to see the slight blush that had crept into his cheeks.

"I can take you to your place now," she said. "Doctors said the LCL hardly affected you. You know, you got pretty lucky with that."

"Sure," said Shinji, half-listening. Misato did not let his seeming mental distance deter her.

"You rated private quarters, you know. Is that... okay?" Shinji didn't respond. "You know, if you ask, I'm sure they'd let you live with your dad. It can easily-"

"No," stated Shinji flatly. "Alone is fine. Less people around the mutant the better. Besides, my father doesn't want me around."

"Oh come now," said Misato, a bit of a nervous edge coming to her voice, "you can't mean that! It's only natural for parents and children to want to live together! If you want to, don't hold back, just ask and-"

"I said NO!" Shinji exclaimed, his hackles rising a bit. "Please leave me alone!"

"What's with the tone?" asked Misato, shocked and a little angered. "I'm just worried about you Shin-"

"Don't you have enough to worry about besides a mutant kid who wants to be left alone?" Shinji asked, frustrated that the purple-haired woman simply would not leave him be.

"So gloomy," she said, so suddenly deadpan that Shinji stopped and turned around. "I'll fix that attitude of yours." Shinji was paralyzed. Misato, he could tell, was angry. So angry that her face had turned into an expression he'd never seen before. She looked calm, but her eyebrow's were arched in irritation, and the veins in her forehead were bulging out. Shinji literally could not move.

Misato whipped out her cell-phone and quickly dialed a number. The other end answered, and Misato spoke. "Hey Ritz, it's me. Hey, Shinji's going to come live with me, ok?"

"What?" Shinji heard over the phone, Ritsuko's voice denoting shock and confusion.

"M-Misato!" exclaimed Shinji.

"Oh don't worry," said Misato, reacting to something Shinji hadn't heard Ritsuko say. "I'm not that desperate. He's just a kid. Now be a dear and get me the proper approval from upstairs." She grinned widely and hung up, Shinji hearing the last indignant words from Ritsuko.

"HOLD ON! CAPTAIN KATSURAGI!" *click*

"Now that's taken care of," said Misato happily, "you'll be coming with me."

"But-"

"Now," she said, the dread expression returning. "What part of 'commanding officer' don't you get?"

888

"Woohoo!" They were speeding down the road, and Misato seemed to be enjoying herself. "We're gonna have all kinds of fun!" she promised, grinning ear to ear. "We should totally celebrate. Pick up some food, party-"

"What's there to party about?" asked Shinji, interrupting.

"Welcoming party," said Misato, as if it were the most obvious thing in the world. "To welcome my new housemate." Shinji looked glum as ever.

"Forgive me if I'm not in the mood," he said, looking out the window. Misato frowned, and looked at one of the upcoming signs. She made a quick and sudden detour. "Hey, what're you-?"

"You need to see something," answered Misato. They took the exit, and drove uphill. They arrived at some kind of scenic roadstop and got out of the car. Misato walked over to the guard rail and waited. Shinji walked over to join her.

"Why are we here?" he asked.

"Just watch," smiled Misato pointing out at the city. It seemed small. Suddenly, things began to move.

Shinji watched in wide-eyed amazement as buildings began rising from the ground. The city expanded, growing and growing to three or four times the size he'd first seen it.

"That," said Misato proudly, "is Tokyo-3! The future of mankind! The Anti-Angel fortress! Our city! But most of all, the city you defended, Shinji."

"Please," he said, frowning, "don't make it something it isn't. It wasn't as heroic as you make it sound. I didn't do it for the good of the city, and it wasn't just to protect that girl either. I just..."

"I know, Shinji," said Misato, putting her hand on his shoulder. "But regardless of any reason you may have had, you still did it. You did really well, and you saved all of our lives. You should have more confidence in yourself. I'm really proud of you."

"..."

"Shinji?" Shinji's eyes began watering, and soon tears were rolling down his cheeks. "Oh no, I'm sorry! Did I say something wrong, Shinji?"

"No, Misato, you didn't," said Shinji, trying to keep his voice steady. She put her arms around him and squeezed his shoulders. "I just... I just wanted to hear those words from him."

* * *

And there it is, folks. The fight you've all been waiting to see. Prepare for new characters in the next chapter! I've already introduced a few mutants, but I'll keep the who's who to myself just a while longer. I've had peoples' powers planned for a while now. If you'd like, please go ahead and guess. You'll know soon enough wether you were right :)

Stay tuned!


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